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BIOCHEMISTRY
Timetables can be accessed at: http://timetable.ucc.ie/1213/department.asp
Click on Biochemistry
For information on building codes click on: http://timetable.ucc.ie/1213/buildingcodes.asp
Autumn Semester/Teaching Period 1 Modules – Period 1A (Monday, 24th
September – Friday, 2nd November)
BC2001 Biomolecules
(5 credits; Teaching Period 1A)
BC3001 Structural Biochemistry
(5 credits; Teaching Period 1A)
BC3003 Introduction to Cell Biology and Biomembranes
(5credits; Teaching Period 1A)
Autumn Semester/Teaching Period 1 Modules – Period 1B (Monday, 5th
November – Friday, 14th December)
BC2002 Principles of Metabolic Pathways
(5 credits; Teaching Period 1B)
BC3004 Cell Signalling
(5 credits; Teaching Period 1B)
BC3006 Molecular Biology
(5 credits, Teaching Period 1B)
Spring Semester/ Teaching Period 2 Modules – Period 2A (Monday, 7th
January – Friday, 15th February)
ML2001 Introductory Molecular Biology
(5 credits; Teaching Period 2A)
BC3002 Advanced Metabolism
(5 credits; Teaching Period 2A)
BC3007 Principles of Medical Genetics
(5 credits, Teaching Period 2A)
BC3010 Bioinformatics
(5 credits, Teaching Period 2A)
Spring Semester/ Teaching Period 2 Modules – Period 2B (Monday, 18th
February – Thursday, 28th March)
BC3005 Biochemical Immunology
(5 credits; Teaching Period 2B)
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BC3008 Biochemistry of the Central Nervous System (5 credits, Teaching Period 2B)
BC3011 Forensic Genetics and Molecular Biology
(5 credits; Teaching Period 2B)
BIOCHEMISTRYMODULE DESCRIPTIONS
Biochemistry is part of the School of Life Sciences at UCC. It is committed to excellence in
education, training and research. Additional information is available at
http://www.ucc.ie/ucc/depts/biochemistry/
The Biochemistry Department is located in three different buildings: Western Gateway
Building, the BioSciences Research Institute and the Cavanagh Pharmacy Building
(http://www.ucc.ie/en/visitors/maps/) . The
Biochemistry
administration
office
(email:
[email protected]; tel:021 4205415) and the undergraduate teaching laboratory (3.29) are
located in the Western Gateway Building .
Each Teaching Period is divided into two six week teaching blocks. In Teaching Period 1
Period 1A runs from Monday, September 24th to Friday, November 2nd. Period 1B runs from
Monday November 5th to Friday, December 14th. In Teaching Period 2 Period 2A runs from
Monday, January 7th to Friday, February 15th. Period 2B runs from Monday, February 18th to
Thursday, March 28th.
Modules at the first year level are not available to visiting students. Modules specific to the
Medical, Dental and Pharmacy degree programmes (BC1024, BC1443, BC2103, BC2443,
BC3443) are also not available to visiting students. Modules available are as follows:
Autumn Semester/Teaching Period 1 Modules – Period 1A (Monday, 24th
September – Friday, 2nd November)
BC2001 Biomolecules
(5 credits; Teaching Period 1A)
Stereoisomers-The concept of stereoisomers and how such molecules can have different
properties despite having the same chemical formula. Examples of pharmaceutical products
are used to illustrate concept.
Water and pH-The role of water as a biological constituent of life. The concept of pH and its
importance to biological systems. Hydrogen bonding. Amino acids-An outline of the structure
and function of amino acids with a focus on their chemical properties and how they can link
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together to form proteins. Protein structure & function -Understanding primary, secondary,
tertiary and quaternary protein structure with detailed examples of how such structures are
dependent on amino acids sequence.
Enzymes and enzyme kinetics-Introduction to the concept of enzymes and their function
including the role of the active site of the enzyme. Introduction to enzyme kinetics. The
concept of enzyme inhibition and inhibitors.
Carbohydrates and polysaccharides-Monosaccharides structure and function. Formation of
simple polysaccharides. Lipids-Structure and function of simple lipids. Role of lipids in biology.
Introduction to Biomolecules. Water ionisation, interaction with biomolecules, pH. Amino
acids: structure, function, classification and reactivity. Introduction to proteins. Protein
structure: primary, secondary, tertiary and quaternary structures. Lipids: structure and
function. Carbohydrates: structure and function. (Staff).
By the end of this module the student should be able to:
Describe the basic principles of stereoisomers and their importance in determining
the chemical and physical properties of compounds
Outline the role of water and pH and describe how hydrogen bonds are formed
Discuss the structure and function of amino acids and in particular how they can
combine to form proteins
Describe the characteristics of the different levels of protein structure and how such
characteristics relate to the amino acid sequence
Describe what an enzyme is and the basis of its function. The student should also be
able to understand basic enzyme kinetics and enzyme inhibition patterns of drugs
Discuss the structure of simple monosaccharides and the importance of chiral
carbons
Describe the formation of simple polysaccharides
Describe simple and more complex lipids and some of their roles in biology
Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous
Assessment 40 marks ((Lab work 10 marks; MCQ 30 marks). Students departing from UCC at
the end of Teaching Period 1 should check with the International Education Office regarding
an assessment for this module.
BC3001 Structural Biochemistry
(5 credits; Teaching Period 1A)
Amino acids, peptides and proteins-Chemistry, structure and classification of amino acids,
The peptide bond, Peptide structure and bioactive peptides, The protein structural hierarchy
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with examples. Isolation of informational biomacromolecules. Precipitation of proteins,
Chromatography of proteins including mode (ion exchange, size exclusion and affinity) and
resolution (HPLC and FPLC), Protein purification tablets, Alkali-phenol lysis for preparation of
plasmid DNA, Isolation of mRNA by oligo dT-cellulose. Sequencing of informational
biomacromolecules-Direct sequencing by Edman degradation, Sequencing of proteins by
mass spectrometry, Sanger sequencing of DNA, Sequence databases. Solid Phase methodsMerrifield
peptide
electrophoresis,
SDS
synthesis,
PAGE,
Synthesis
Isoelectric
of
oligonulceotides.
focusing,
2D
SDS
Electrophoresis-Native
PAGE,
Blotting
methods,
Electroelution. Enzymes Purification of organelles, membranes and membrane proteins from
cells-Basis of catalysis, Michaelis-Menten equation, Kinetic parameters, Enzyme inhibition.
Allosterism and metabolic control.
By the end of this module you should be able to:
Describe the key structural features of the main informational biomacromolecules
Outline how proteins and DNA plasmids are routinely purified
Discuss the physical and chemical basis of chromatography
Describe how important sequence is to function
Appreciate the origin and use of sequence data
Describe the basis and application of electrophoresis methods in Biochemistry
Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous
Assessment 40 marks (Lab work 10 marks; Data Handling test 10 marks; MCQ 20 marks).
Students departing from UCC at the end of Teaching Period 1 should check with the
International Education Office regarding an assessment for this module.
BC3003 Introduction to Cell Biology and Biomembranes
(5 credits; Teaching Period 1A)
Introduction to cell biology; The structure of eukaryotic cells; The structure and functions of
organelles; Importance of biomembranes from an evolutionary perspective; Organization of
membranes in eukaryotic cells; Membranes and membrane proteins; Structure, lipid
composition and properties of biological membranes; Classification: Integral, lipid anchored,
peripheral membrane proteins; Structural features of integral membrane proteins; Transport
of ions and small molecules across membranes; Membrane permeability, electrical and
chemical gradients across membranes; Membrane Transport Proteins: ATP powered pumps,
Ion channels, Transporters; The cellular cytoskeleton; Microfilaments, Microtubules and
intermediate filaments; Structure and Properties of different cytoskeletal elements; The
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cytoskeleton in specialized cell types; Cellular Logistics: Targeting proteins to membranes and
organelles; Targeting proteins to the endoplasmic reticulum; Transport of proteins across the
nuclear envelope; Targeting of proteins to other organelles; Vesicular Trafficking; The
secretory pathway and endocytic pathways; Protein quality control: Protein ubiquitintion and
degradation; Purification of organelles, membranes and membrane proteins from cells
Subcellular fractionation of cells by differential centrifugation; Purification of membrane
proteins.
On successful completion of this module, students should be able to:
Describe the organization and functions of membranes and organelles in eukaryotic
cells
Distinguish between different classes of membrane-associated proteins
Outline the general structural features of integral membrane proteins
Review the major classes of proteins involved in transport of small molecules across
membranes
Discuss the role of the different cytoskeletal elements in a variety of cell types
Apply bioinformatics tools to identify targeting motifs in a protein
Compare the mechanisms by which newly synthesized proteins are targeted to the
major organelles in eukaryotic cells
Illustrate how proteins are trafficked within the secretory and endocytic pathways
Explain and apply the principles of subcellular fractionation
Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous
Assessment 40 marks (Lab work 10 marks; MCQ 30 marks). Students departing from UCC at
the end of Teaching Period 1 should check with the International Education Office regarding
an assessment for this module.
Autumn Semester/Teaching Period 1 Modules – Period 1B (Monday, 5th
November – Friday, 14th December)
BC2002 Principles of Metabolic Pathways
(5 credits; Teaching Period 1B)
General introduction to types of metabolic pathways and common strategies used in energy
metabolism, bioenergetics. Overview of carbohydrate and lipid metabolism. Glycolysis,
gluconeogenesis, glycogen metabolism and the regulation of these pathways, discussing
hormonal, covalent and allosteric control of enzymes. The citric acid cycle and its central
role in metabolism. Oxidative phosphorylation, electron transfer and ATP synthesis. Lipid
metabolism. The mobilization of fats. Fatty acid catabolism. Ketone body formation. Fatty
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acid biosynthesis. Regulation of fatty acid and lipid metabolism. Integration and overall
control of metabolism. (Staff).
On successful completion of this module the student should be able to:
Outline how energy is harvested and used to drive cellular reactions
Describe and illustrate the metabolic pathways of glycolysis, glycogenolysis,
gluconeogenesis, the citric acid cycle, oxidative phosphorylation, the synthesis and
degradation of fatty acids and the synthesis of ketone bodies
Describe the interrelationships between the various metabolic pathways and outline
their overall regulation
Proficiently perform laboratory experiments and record, analyse and evaluate data
obtained
Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous
Assessment 40 marks (Lab work 10 marks; MCQ 30 marks). Students departing from UCC at
the end of Teaching Period 1 should check with the International Education Office regarding
an assessment for this module.
BC3004 Cell Signalling
Hormone/Neurotransmitter
(5 credits; Teaching Period 1B)
classification. Steroids
and
tyroxine. Polypeptides: growth
hormones, insulin, glucagon. Amino acid-derived, classical neurotransmitters. Eicosanoids.
Cell/Cell signalling. Diversity of receptor types. Classification and biochemistry of cell surface
receptors.
Hierarchical
nature
of
hormonal
control.
Signalling
in
response
to
steroids/thyroxine, intracellular receptor/ transcriptional regulation. Signalling via G-proteins
and tyrosine kinases. Second Messengers: cAMP, IP3/DAG: synthesis, generation in cell.
Protein Kinase C. Heterotrimeric G-protein role in signal transduction/sensory perception in
various cell types. Signalling via ligand gated ion channels. Small GTPases. Signal
transduction and oncogenesis. (Staff).
On successful completion of this module the student should be able to:
Describe the major mechanisms of cell/cell signaling in humans, including the
hierarchical nature of the neuroendocrine system
Describe the mechanism of action of the major functional groups of signaling
molecules, including polypeptides (growth hormones, insulin, glucagon), steroids,
thyroxine, retinoic acid, amino acid derived signaling molecules, classical
neurotransmitters & eicosanoids
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Outline the major receptor types, their localization and function in response to the
signaling molecules indicated in the point above
Discuss the molecular events which occur within the cell in response to the major
groups of signaling molecules and the overall physiological outcomes
Discuss signal transduction events occurring in sensory perception, such as in vision,
smell & taste
Describe the structure and function of GAP junctions
Outline the relationship between growth signal transduction and cancer
Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous
Assessment 40 marks (Lab work 10 marks; MCQ 30 marks). Students departing from UCC at
the end of Teaching Period 1 should check with the International Education Office regarding
an assessment for this module.
BC3006 Molecular Biology
(5 credits; Teaching Period 1B)
DNA structure and function; DNA supercoiling; chromatin and higher order structure and
organization in eukaryotic DNA; RNA transcription in prokaryotes and eukaryotes; eukaryotic
gene regulation with respect to chromatin; gene promoters; prokaryotic and eukaryotic
gene regulatory mechanisms at transcriptional and translational level; RNA splicing and
alternative splicing; molecular mechanisms of recombination; DNA amplification and DNA
analysis technology; recombinant DNA technology and its applications including protein
over expression.
On successful completion of this module, students should be able to:
Describe the structure and function of DNA, DNA supercoiling and the molecular
mechanisms of its enzymatic regulation
Describe chromatin and higher order structure and organisation in eukaryotic DNA
and demonstrate an understanding of chromatin in gene expression and regulation
Outline the main principles of gene regulation in prokaryotes and eukaryotes
Describe using examples a range of prokaryotic and eukaryotic gene regulatory
mechanisms
Describe the molecular mechanisms of RNA splicing and demonstrate an
understanding of alternative splicing
Describe the molecular mechanisms of recombination and demonstrate an
understanding of the role of recombination in prokaryotes and eukaryotes
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Describe the process of DNA amplification and DNA analysis technology relevant to
gene regulation analysis.
Describe recombinant DNA technology and its applications including protein over
expression
Demonstrate competence in performing Molecular Biology techniques and
understanding their basis and application
Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous
Assessment 40 marks ((Lab work 10 marks; MCQ 30 marks). Students departing from UCC at
the end of Teaching Period 1 should check with the International Education Office regarding
an assessment for this module.
Spring Semester/ Teaching Period 2 Modules – Period 2A (Monday, 7th
January – Friday, 15th February)
ML2001 Introductory Molecular Biology
(5 credits; Teaching Period 2A)
Genes and Genomes. DNA replication, DNA repair, RNA transcription and processing.
Genetic code, and protein synthesis. Gene regulation, lac operon. Gene cloning, the tools
and strategies. Polymerase chain reaction (PCR) and its applications.
On successful completion of this module, students should be able to:
Compare and contrast the structure of the nucleic acids, DNA and RNA and
prokaryotic and eukaryotic genes
Describe the molecular mechanisms of replication, transcription, translation
Describe the different types of post-transcriptional and post-translational
modifications
Describe the causes and nature of DNA mutations, the pathways used to repair DNA
damage, and the consequences of failing to repair DNA damage
Describe the structure of an operon and how its expression can be regulated
Identify gene regulation and understand a number of different mechanisms of
regulation
Identify and understand some Molecular Biological technologies, e.g. PCR, cloning,
Southern blotting
Demonstrate competence in performing basic Molecular Biology and Microbiology
techniques and understanding their basis and application
Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous
Assessment 40 marks (Laboratory Work 10 marks; MCQ 30 marks
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BC3002 Advanced Metabolism
(5 credits; Teaching Period 2A)
Overview of Nitrogen Metabolism. Nitrogen Fixation. Nitrogen Cycle. Metabolic fates of
amino groups. Role of Glutamate. Elimination of Ammonia. Pathways of Amino Acid Synthesis
and degradation. Metabolism of biogenic amines. Review of structure of principal
nucleotides and their functions. Metabolism of purines and pyrimidines: Synthesis and
catabolism. Salvage pathways. Chemotherapeutic agents that target enzymes in the
nucleotide biosynthetic pathways. Integration of hormonal regulation of mammalian
metabolism. Biosynthesis of membrane lipids and related substances. Cholesterol
Metabolism. Biosynthesis. Lipoprotein metabolism. Bile acid metabolism. Steroid hormone
metabolism.
On successful completion of this module the student should be able to:
Describe and illustrate the metabolic pathways of purine, pyrimidine and amino acid
metabolism
Describe and illustrate the enzymology of nitrogen fixation
Describe and illustrate the Biochemistry of the polypeptide and steroid hormones
Illustrate the structure of principal nucleotides and their functions
Discuss chemotherapeutic agents that target enzymes in the nucleotide biosynthetic
pathways
Describe the biosynthesis of principal membrane lipids
Outline cholesterol, lipoprotein and bile acid metabolism
Describe the interrelationship and regulation of the various metabolic pathways
Proficiently perform laboratory experiments and assess the laboratory data recorded
Assessment: Total Marks 100: End of Year Written Examination 70 marks; Continuous
Assessment 30 marks (MCQ 30 marks).
BC3007 Principles of Medical Genetics
Meiosis,
homologous
recombination,
(5 credits; Teaching Period 2A)
resolution
of
Holiday
structures,
illegitimate
recombination. Genetic disease patterns, autosomal dominant, recessive, X linked,
penetrance, polygenic, genetic imprinting. Population genetics, polymorphism/genetic
variation, Hardy-Weinberg equilibrium, factors affecting allele frequencies. Quantitative traits,
twin studies,heritability. Cytogenetics analysis, chromosome abnormalities and related
studies. Molecular markers, RFLPs, VNTRs and micro-satellites, DNA fingerprinting. Basis of
genetic mapping and positional cloning. Genetic association studies. Cancer genetics.
Production of mouse mutants. Human gene therapy.
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On successful completion of this module, students should be able to:
Describe the key molecular and cellular processes that occur during meiosis, and
explain how Holliday junctions determine the types of recombinant DNA molecules
that are produced
Distinguish between different classes of autosomal and sex-linked inheritance
patterns, and list the different types of mutations that contribute to human disease
Review the history and development of the different types of molecular markers used
in genetic analysis
Define and discuss key concepts such as quantitative traits, heritability, twin studies,
genetic mapping
Outline the factors affecting allele frequencies in populations
Discuss the underlying theory and practical pursuit of genetic association studies
Outline the molecular basis of selected human genetic diseases including cancer
Outline general approaches to the use of model organisms in the study of human
disease
Discuss the current status of the various options for pursuing human gene therapy
Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous
Assessment 40 marks (Lab work 10 marks; MCQ 30 marks).
BC3010 Bioinformatics
(5 credits; Teaching Period 2A)
Introduction to computers. The Internet. Sequence alignment; dynamic programming, profile
alignment, multiple alignment, Molecular biology databases; nucleotide sequences, amino
acid sequences, derived databases, genetic databases, protein structure databases.
Database similarity searches. Phylogenetic analysis and molecular evolution, protein
structure prediction. Gene finding.
On successful completion of this module, students should be able to:
Outline the broad area of bioinformatics and why it is of emerging importance in
biosciences research
Describe how to find and use a wide range of bioinformatics databases and
resources for gene analysis
Describe the processes by which genomes, DNA, RNA and protein molecules change
over evolutionary time
Discuss how alignments and phylogenetic trees are built
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Describe the different types of selection pressures that can act on coding and noncoding DNA
Describe the evolutionary basis for comparative genomics
Describe the emerging "omics" technologies, including genomics, proteomics and
metabolomics
Proficiently conduct some bioinformatics research and develop presentation skills for
their own work and a research paper
Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous
Assessment 40 marks (Practical problem solving 5; Project write-up and presentation 35).
Spring Semester/ Teaching Period 2 Modules – Period 2B (Monday, 18th
February – Thursday, 28th March)
BC3005 Biochemical Immunology
(5 credits; Teaching Period 2B)
Historical development of immunology, Innate and acquired immunity. Cells and organs of
the immune system. Antibody structure & function MHC, Antibody based assays and
methods, Antigen processing and presentation, Antigen receptors and signaling, Generation
of antibody diversity. Immunologic tolerance. Transplantation immunology. Autoimmunity.
(Staff).
On successful completion of this module, students should be able to:
Illustrate the development of the field of immunology as a science
Describe development and function of the innate and adaptive immune systems
Describe the tissues and cells of the immune system and how they are integrated
Describe the structure and function of antibodies and how they interact with
antigens
Outline the uses of antibodies in diagnostic and analytical assays
Explain the role and function of the MHC and how antigens are processed and
presented by cells of the immune system
Explain how a diverse range of antibody molecules can be produced
Describe the basis of immunological tolerance, the role of the immune system in
organ transplantation and autoimmune diseases
Demonstrate competence in performing and understanding antibody based
staining and assay techniques
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Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous
Assessment 40 marks.
BC3008 Biochemistry of the Central Nervous System (5 credits; Teaching Period 2B)
Structure and function of neurons and glia. Basic anatomy of the central nervous system
(CNS). Information transfer in the CNS. The molecular basis of the action potential,
neurotransmission and synaptic function. The molecular basis of neurotransmitter release,
examination
of the key proteins involved
in this process and current
research.
Neurotransmitter classification and description of the major neurotransmitters, their
localization, function, receptors and transporters. Neurotransmitter transporters: structure and
function. Neurotransmitter receptors: structure and function. Detailed consideration of
neurotransmission by acetylcholine, serotonin, glutamate and GABA. Key defects in
neurotransmitter signalling that lead to brain malfunction for example in stroke, Parkinson's
disease, depression, and psychiatric disorders. Throughout the course emphasis is based on
the key techniques in molecular neuroscience that are used to understand the molecular
basis of neurotransmission and brain function.
On successful completion of this module students should be able to:
Describe and illustrate the structure and function of the key brain cell types and the
major neuroanatomical regions of the central nervous system
Explain how information is transferred by neurons and the molecular basis of the
action potential, neurotransmission and synaptic function
Describe the molecular basis of neurotransmitter release and the function of the key
proteins involved in this process
Outline and illustrate the structure and function and mechanisms action of
neurotransmitter transporters and neurotransmitter receptors
Review the major neurotransmitter types, their receptors, transporters, function and
localisation in the brain
Explain in detail neurotransmission by acetylcholine, serotonin, glutamate and GABA
Outline key defects in neurotransmitter signalling that lead to brain malfunction
Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous
Assessment 40 marks (Lab work 10 marks; MCQ 30 marks).
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BC3011 Forensic Genetics and Molecular Biology
(5 credits; Teaching Period 2B)
The history and science of human identification; DNA, RNA and protein; the molecular basis
of hereditary; the human genome: the molecular basis of human and genome diversity; the
genome and forensic genetics; DNA fingerprinting (minisatellites, microsatellites, STRs) and
profiling; paternity testing; basic principles in population genetics; forensic anthropology:
mitochondrial and Y chromosome analysis in forensic science; forensic and genealogical
investigations; DNA databases; ethical issues: DNA extraction and DNA amplification
technology; case studies in forensic DNA, genetics and molecular biology.
On successful completion of this module, students should be able to:
Describe the main principles of forensic genetics and relevant molecular biology
Outline DNA amplification and DNA analysis technology relevant to forensic
applications
Outline the molecular basis of hereditary
Describe the basis of human and genome diversity and relatedness
Describe the main types of DNA variation found in genomes
Describe how DNA variations behave in human populations and an understanding
of the factors influencing such behaviour
Describe DNA fingerprinting and DNA profiling and its application in forensic science
Outline the applications of mitochondrial and Y chromosome analysis in forensic
science
Assessment: Total Marks 100: End of Year Written Examination 70 marks; Continuous
Assessment 30 marks (MCQ).
Modules at the fourth year level are not available to visiting students.
Please note that prospective visiting students must make their application to study particular
modules though the International Education Office.
Email: [email protected]
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